Add descriptions - picrust/picrust2 GitHub Wiki

add_descriptions.py is a convenience script that will add a column to your table of gene family or pathway abundances corresponding to a quick description of each functional category. These descriptions are in picrust2/default_files/description_mapfiles. You can also use custom mapping files.

To add a description column to E.C. number, KO, and MetaCyc pathway abundance tables respectively:

add_descriptions.py -i EC_metagenome_out/pred_metagenome_unstrat.tsv.gz -m EC \
                    -o EC_metagenome_out/pred_metagenome_unstrat_descrip.tsv.gz

add_descriptions.py -i KO_metagenome_out/pred_metagenome_unstrat.tsv.gz -m KO \
                    -o KO_metagenome_out/pred_metagenome_unstrat_descrip.tsv.gz

add_descriptions.py -i pathways_out/path_abun_unstrat.tsv.gz -m METACYC \
                    -o pathways_out/path_abun_unstrat_descrip.tsv.gz

Note that as of PICRUSt2-v2.6.0, this script works with the PICRUSt2-SC database. If you are using it with the old database, you can run add_descriptions_oldIMG.py in exactly the same way as described here.

Arguments/options:

• -i: Input function abundance table.
• -o: Output function abundance table with added description column.
• -m: Mapping table to use (if one of the default tables should be used).
• --custom_map_table: Custom mapfile to use if using a non-default function database.